Variant report

Variant	rs10485767
Chromosome Location	chr20:13753470-13753471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13751498..13754667-chr20:13763599..13766758,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12625600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs28680787	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3789336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813143	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4814253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs59453142	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6105160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6105163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6105169	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6110019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs6110023	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs6110030	0.90[EUR][1000 genomes]
rs6110037	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6110050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6514441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7360405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7363551	0.86[EUR][1000 genomes]
rs736365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
2	chr20:13734000-13763200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr20:13736800-13763800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:13740800-13757600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr20:13741800-13763200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr20:13741800-13763800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:13742000-13757600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr20:13742000-13757800	Strong transcription	NH-A	brain
9	chr20:13742000-13759000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr20:13742000-13762600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:13742200-13763600	Strong transcription	Liver	Liver
12	chr20:13742400-13763800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr20:13743800-13758000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr20:13743800-13758200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr20:13743800-13763600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr20:13744000-13758200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr20:13744400-13758600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:13744400-13763200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr20:13744800-13753800	Strong transcription	Fetal Thymus	thymus
20	chr20:13745000-13757600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:13746400-13757600	Strong transcription	HMEC	breast
22	chr20:13746800-13758000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:13747000-13753600	Strong transcription	Fetal Kidney	kidney
24	chr20:13747200-13758200	Strong transcription	A549	lung
25	chr20:13747200-13759400	Strong transcription	HepG2	liver
26	chr20:13747200-13764000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:13747600-13754200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr20:13747600-13758600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr20:13747600-13759000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr20:13747600-13759200	Strong transcription	Fetal Intestine Large	intestine
31	chr20:13747600-13764400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr20:13747800-13753800	Strong transcription	NHDF-Ad	bronchial
33	chr20:13747800-13757400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr20:13747800-13759000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr20:13747800-13763800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr20:13748000-13759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr20:13748000-13763200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr20:13748000-13763800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr20:13748400-13764000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:13748600-13763400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:13748800-13763800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr20:13748800-13764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr20:13749000-13756400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr20:13749000-13756400	Weak transcription	Psoas Muscle	Psoas
45	chr20:13749000-13757000	Weak transcription	Fetal Heart	heart
46	chr20:13749000-13760600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr20:13749000-13764000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:13749000-13764200	Weak transcription	Aorta	Aorta
49	chr20:13749000-13764200	Weak transcription	Colonic Mucosa	Colon
50	chr20:13749000-13765200	Weak transcription	Small Intestine	intestine

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